Variant report

Variant	rs4738886
Chromosome Location	chr8:62278767-62278768
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	IKZF1	chr8:62278234-62279237	GM12878	blood:	n/a	n/a
2	FOS	chr8:62278288-62280006	MCF10A-Er-Src	breast:	n/a	chr8:62279057-62279066 chr8:62279053-62279064 chr8:62279541-62279549 chr8:62279055-62279067 chr8:62279058-62279065 chr8:62279057-62279065 chr8:62279055-62279062 chr8:62279785-62279794
3	SMC3	chr8:62278753-62279227	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:62278733..62281370-chr8:62291248..62293763,2	K562	blood:

Variant related genes	Relation type
CLVS1	TF binding region

Extended variants
information (count: 73 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10093364	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10094365	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10098539	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10098755	1.00[CHB][hapmap];0.95[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs10098885	1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs10099169	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10100364	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10111649	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs10111651	1.00[CHB][hapmap];0.95[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs10112069	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs10957192	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs12546667	0.82[ASN][1000 genomes]
rs12675558	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12676622	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12679865	0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1371741	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1371744	0.83[CHB][hapmap]
rs1486648	0.81[TSI][hapmap]
rs16927201	1.00[ASN][1000 genomes]
rs16927234	0.98[ASN][1000 genomes]
rs16927237	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs16927280	0.95[ASN][1000 genomes]
rs16927291	0.94[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs16927299	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs17775880	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1822032	0.83[CHB][hapmap];0.82[CHD][hapmap]
rs1873888	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1992331	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1992332	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1992333	1.00[CHB][hapmap];0.95[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2201261	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap]
rs2220766	1.00[CHB][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap]
rs2610519	0.83[CHB][hapmap];0.87[CHD][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs28419747	0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28477525	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28533992	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28886409	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3864676	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4147444	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4147445	1.00[CHB][hapmap];0.92[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4147446	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4395891	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4737584	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4737585	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4737586	0.92[ASN][1000 genomes]
rs4738885	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4738887	0.92[ASN][1000 genomes]
rs4738888	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4738889	0.93[ASN][1000 genomes]
rs56079904	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56161034	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59241236	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62524926	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6471947	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs6471949	0.98[ASN][1000 genomes]
rs6983659	1.00[CHB][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs6987161	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6994385	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6994804	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6998442	0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7012230	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs72657057	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7386996	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7820685	1.00[CHB][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7836228	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948922	chr8:61818964-62475097	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv1024432	chr8:62086247-62898782	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv831336	chr8:62188396-62364873	Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv1027742	chr8:62206883-62613533	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv539633	chr8:62206883-62613533	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
6	nsv1021377	chr8:62214279-62596721	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
7	nsv539634	chr8:62214279-62596721	ZNF genes & repeats Genic enhancers Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
8	nsv1029046	chr8:62224341-62535277	Strong transcription Enhancers ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4738886	CLVS1	cis	cerebellum	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:62263600-62279000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr8:62270800-62290200	Weak transcription	Fetal Brain Female	brain
3	chr8:62278200-62279200	Flanking Active TSS	GM12878-XiMat	blood
4	chr8:62278200-62280200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr8:62278400-62279000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr8:62278400-62280400	Enhancers	Adipose Nuclei	Adipose
7	chr8:62278600-62280200	Weak transcription	Fetal Brain Male	brain

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